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Wells was born in Trenton, New York, a member of the sixth generation of his family in America. His original immigrant ancestor was Thomas Welles (1590–1659), who arrived in Massachusetts in 1635 and was the only man in Connecticut's history to hold all four top offices: governor, deputy governor, treasurer, and secretary. A few years after the death of his father in 1826, Daniel H. Wells left New York with his mother Catherine Chapin Wells and his younger sister Catherine C. Wells and moved to Illinois.

Wells arrived in Hancock County, Illinois, in 1835. He lived in Commerce, Illinois—later renamed Nauvoo—and was a major landowner and justice of the peace there for several years prior to the arrival of large numbers of Latter Day Saints in 1839.

Although not a member of the Latter Day Saints, Wells was considered by opponents of the church to be a "Jack Mormon", a term originally applied to non-members who were friendly to or defended the Latter Day Saints. In Nauvoo, he served on the city council and as a judge.

Mobs invaded Nauvoo after the assassination of church founder Joseph Smith; Wells defended the city and fought as a Lieutenant General of the Nauvoo Legion, and also provided shelter for evacuees. Wells was not baptized into the LDS Church until August 9, 1846. He emigrated to the Salt Lake Valley with the Mormon pioneers in 1848.

Well respected for his integrity and loyal service, he was elected Attorney General of State of Deseret in 1849. When Jedediah M. Grant died in 1856, Wells was ordained an apostle of the LDS Church and set apart as Second Counselor to Brigham Young in the First Presidency of the church. Although serving as an apostle, Wells was never sustained as a member of the Quorum of Twelve Apostles. Upon Young's death in 1877, Wells was sustained as a Counselor to the Quorum of the Twelve Apostles, a position he held until his death.

From 1848 until 1863, Wells was superintendent of public works for the LDS Church and presided over the continuing construction of the Salt Lake Temple (completed 1893) and the Salt Lake Tabernacle (completed 1867). When Wells was no longer in the position, the operation of the church's public works program was placed under the supervision of the Presiding Bishopric.[3]

In 1866, Wells was elected mayor of Salt Lake City as a member of the newly formed People's Party; he was re-elected in both 1872 and 1874. In 1871, he was arrested by U.S. marshals on charges related to polygamy. Wells served twice as president of the European Mission of the LDS Church, first in 1864–65 and again in 1884–87.

Wells married Eliza Rebecca Robison in 1837 and with her had one son, Albert Emory Wells. His wife refused to accompany Wells to Utah in 1848 and later divorced him. Between 1849 and 1852, Wells married six additional wives: Louisa Free, with whom he had eight children; Martha Givens Harris, with whom he had seven children; Lydia Ann Alley, with whom he had six children; Susan Hannah Alley, with whom he had four children; Hannah Corilla Free, with whom he had eight children; and Emmeline Belos Woodward, with whom he had three children. Louisa Free, Hannah Free, and Emmeline Woodward were all previously married and divorced or widowed. Each had one or more children whom Wells adopted and reared as his own.